The Two Sides of Maes Hughes
by Nicholas Perle
Summary: (AU after ep 25. Total WIP, totally overhauled). Loss is the curse of an alchemist, driving them to rash decisions and dangerous experiments, especially when the temptation is laid out...
1. The Beginning

The Two Sides of Maes Hughes

- (AU but full of spoilers for the anime and manga. Also very much a WIP. Consider yourself warned). Loss is the curse of an alchemist, driving them to rash decisions and dangerous experiments, especially when the temptation is laid out to them by someone else. But what are the consequences? (Now with a hundred percent more flashbacks and alchemical theory!)

Author's Notes:

One: FullMetal Alchemist is not mine. Roy Mustang and Maes Hughes are also not mine. The other characters from the anime are not mine. The plot... ok, at least that's mine, as twisted as it is. Oh, and this leaves off awkwardly, partly because I'm evil like that, and partly because I wanted to get it up on Oct. 3rd. (-:

Two: This is your final warning. This fic takes place right after episode 25, and contains (mostly minor) spoilers for a lot of episodes since then. The manga is my friend, especially its timeline, so don't be surprised if the story follows that more faithfully than the show.

Three: So, after a bit of deliberating I've decided that my original screwed-up plot twist was too screwed up for me to take the story entirely seriously. So, I sat down and pretty much doubled the entire thing without getting any further on the plot. (My logic works that way). I honestly wasn't expecting any reviews for this... so thank you! It rather inspired me to try to make this suck less. (-: And as before, all reviews are welcome and encouraged and I'll love you, unless you flame me, in which case I'll ignore you but be vaguely amused anyway. Nya!

-- ---- --

Roy Mustang sat alone in his office, staring out into the cloudless sky. It had been two days since the funeral of his best friend, and still the skies refused to rain. The military continued its business outside his door, accustomed to loss. The world continued to turn, mocking him, allowing him to believe he was alone. Roy had thought that throwing himself into his work would help him cope, but his mind continued to wander back to his studies before the Ishbar conflict. There was not an alchemist alive that had not researched the forbidden art of human transmutation or followed the powerful glow of the philosopher's stone. Curiosity and loss together were the curse of the alchemists, dangling the promise of the return of their loved ones just out of their reach, driving them to break the taboo.

The last time he had felt this desperate he had just returned from the war. Everyone was haunted by the war though. Among the officers, the haunting memories also gave them a sense of pride. They had experience. They based their authority on that experience, because they had _been there_, had seen things that most hoped those under them would never have to see. Among many of the State Alchemists who had been stationed in Ishbar, there was a sort of understanding. They all knew that in some way, no matter how forbidden it was, they had the power to undo the things they had done. At the end of the war, when the orders stopped and the discharges handed out, the red stones were also revoked, putting an end to the hopes that the extra power might make their wild plans possible. Nevertheless, a small group of alchemists had tried. Few still remembered, for the evidence had been disposed of long ago. They had been close, in the same unit throughout the war, and had no doubt been planning for quite some time. A few days after their discharges, they had returned to Ishbar to atone for their deeds. Three disappeared entirely. The other two were found with the remains of several unrecognizable bodies. Their autopsies showed that they were missing vital internal organs, though no outward wounds were visible. The entire incident had been written off as a small-scale retaliation by militants then buried deep in the piles of military records. The original documents were still kept in the basement, though only Roy now knew of them. The records floor was full of tiny secrets, squirreled away by the intelligence officers. Maes had been the one ordered to destroy the papers, but Roy had talked him into hiding them, instead - a small tribute to the ones who were brave enough to make the sacrifice, to at least _try_ to make things better. The trade, as Maes insisted, was that he promised not to try the same thing himself. He hoped someday someone would come across the papers and remember, and respect them for what they had done. He sometimes wished that he could have joined them.

Even with Maes Hughes' faithful support, readjusting to life after the war had been hard on Mustang. Rather than simply cleaning the dust out of his apartment and returning to more common work, he had found himself re-reading the alchemy books that lined the walls of his study. It had been especially hard after Tim Marcoh had come to visit. Roy had been amazed to see him appear at his door, thinking that he had long ago sought refuge far from Central. He had always been one to hide things where they would be most obvious, and most hidden, though. It was one of his talents that never ceased to amaze Roy. With a small apologetic smile, he had let himself into the apartment and proceeded to thank Mustang for letting him escape that day in the only way an alchemist knew how.

"_My life is certainly worth my life's work. The best way I can thank you is to pass on what I know to you. I can't expect you to remember it all, or even understand it. But it's the least I can do. You mustn't take notes or anything, there are enough of those already... just listen."_

He went on, outlining what seemed to be everything he knew about alchemy, filling in the areas he knew Roy had never studied. Alchemical healing... using alchemy as a power source... the philosopher's stone, its limits, and its effects. Though Roy didn't note it at the time, he had carefully skirted around the issue of its ingredients.

When Marcoh had finished, Roy had only one question.

"_And... now that you're out of the military, I can ask you this frankly: what about body alchemy? Did your research ever fall into that?"_

Marcoh looked wary, and answered with a sigh.

"_Only the higher-ups knew, but yes, my research was often pushed into the realm of body alchemy. There was... probably still is... an entire lab devoted to the study. Chimeras were never my thing, but they were interested in the power of the red stone, and asked me to research what effect it would have on their work. For the most part, the reactions were almost entirely impossible to control using the stone. We had a bit more success by having the stone _in _the alchemists themselves, usually given to them as a pill, but more often than not there were bad side-efeects to that as well. _In_ the end, I had to substitute a placebo for the stone just so they would stop destroying themselves in their experiments. It was the most horrible thing I've ever had to watch... Brilliant men, throwing themselves into their work, playing God and not caring, only to destroy themselves in the end, sometimes making themselves into the very things they were studying. Rebound has always been a problem. If you do not pay the proper price, it comes back for you. Oh, and the souls..." _ Roy had obviously hit a nerve with his question. The doctor had not wanted to discuss it outright, but seeing Roy's interest he had let the floodgates open.

"_The most important part of alchemy is understanding what it is you're working with. It's why body alchemy is so difficult. It is relatively easy to understand the different elements and how they interact with each other, but within a body, the interactions are far too complex. For each thing you change, there are a thousand other things that are also affected, and it's impossible to tell what they will be. Even if an alchemist understands the body well enough to perform alchemy on animals, he can never do it on humans. The soul comes into play, and its existence is far too complex for any man to understand. Binding a soul is nearly impossible. There is always the risk of rejection, and the alchemist must understand the soul itself on a very intimate level to be able to manipulate it. On top of that, the soul must also understand the alchemist. It is completely impossible to bind a soul that is unwilling. As for the price one must pay... it's also impossible to tell. Very, very few people try this type of alchemy and survive, and almost none of them will talk about the experience afterwards. You saw the pictures of the men in Ishbar. No, you don't nee to pretend you didn't. They all had to sacrifice something. They might have survived if someone had been there for them, but even then I know the military would have just... well, it's probably best that it happened the way it did. But you see the price they had to pay. It's no trifling matter."_

Roy had nodded in a very military fashion at his remark, and Marcoh gave him a concerned look. _"I was afraid of this. You kids had to see too much." _He sighed again, giving Roy a very pointed look. _"It's tough, I know. But as long as you have someone close by your side, helping you out, it'll be fine. Listen, you're a good man, and orders are orders. You followed them _because_ you're a good man. I don't want to have to worry about you. So please be careful, and don't make me feel guilty about this."_ He gazed down at the table briefly. _"The military is really going to need someone like you in the future."_

He got up and left. Roy watched him walk to the door. On the table sat three red pills.

_--_

Roy snapped himself out of his reverie. It was unbecoming of an officer to stare out the window for so long. He had forgotten about Marcoh's little gift, and it surprised him that the thought had now crossed his mind. He knew, however, that as a part of the military, as a State Alchemist whose goal was to push his way to the top of the ranks, he could not risk reviving his friend. Even for the hero of Ishbar, a crime is a crime. He stood, paced the room a few times, scattered some papers across his desk to give the illusion that he had been working, and turned off the lights to leave. With one last look around his office, he turned towards the door... tried it... found it locked.

"What the... my door doesn't lock from the outside..." Mustang stared at the doorknob. "Alchemy..." He swore under his breath, and turned to see a man staring back from the darkest corner of the room.

"I'd advise you not to turn on the lights..." warned the man in an uninterested monotone when he saw Mustang go for the switch. "No fires, either." The man's habit of inserting dramatic pauses so automatically in his speech immediately grated on the Colonel's nerves, and he tried his best to push himself back into his usual military mindset.

"Who do you think you are? You do not have the authorization to enter my office at this hour, especially without talking to my secretary first."

"Don't try to act tough now, Colonel," he said in an almost soothing tone. "Don't think I didn't see you crying earlier. I know how you feel. Thus, I have a proposition for you... I know you've considered it already." The man noted Mustang's quick intake of breath and began to smirk a little.

"I'm only here to give you a little.... encouragement. What if I told you no one would ever find out about your... transgression? It's risk-free, Colonel. Heh... I know Marcoh would never tell you anything like that. Bt it's true. I'll set up the place, and tell you the time. All I need from you is your word. Finish training yourself in human alchemy... I'll seek you out again later."

"But... wait. What interest could you possibly have in bringing him back?"

"It's a close _family_ matter." His emphasis on family was odd, Roy noticed, like it had a second meaning. "I will not explain it any more than that. Suffice it to say I will not betray you to the military. I am not in a position to ask for your trust, though. So I must rely on your own will to do this. For yourself, for Mr. Hughes, and most importantly for his... family."

With that, the figure seemed to disappear. There was a faint glow as the change in the door was undone, and Mustang was free. He shook his head to clear it, took a few breaths to settle his emotions, and walked out the door.

_I should have burnt him to a crisp... Why didn't I?_

--

Later that night, the dark man arrived at his home. Inside, a group of young-looking people dressed in various styles of black attire were waiting for him. The looks in their eyes though, betrayed something that did not quite feel human. Though greeted only by their stares, he was not phased. He simply nodded a greeting, hung up his coat, and took a seat on his couch.

"Is it done?" asked the one youngest in appearance. He had a cruel, mocking smile that seemed to be permanent.

"The seed has been planted. We can only wait."

"You've said that before..."

The only guest in normal clothes – a green dress – stood to address the man. "But, do you really think he can..."

"No. No, of course not." Without his heavy black coat, the man looked much less than menacing, almost jovial. He continued with a laugh. "He is much less powerful than FullMetal, and even he couldn't... No, he will give us exactly what we need. I'm sure you know our current Greed is getting a bit... spoiled. Shall we say, his... expiration date is rather... soon. And we will need a replacement very soon. You all know that the time is coming."

A pair of ravenous red eyes glowed from the corner. "Can I...?"

"No, you may not. He'll meet a more fitting end."


	2. Mystery at the 5th Lab

At his apartment, Mustang's routine had remained unchanged since the funeral. After work, he would return home, maybe make himself dinner if he remembered he was hungry, and then read over papers in his study. More often than not they were old correspondences with Hughes from the war in Ishbar. For the most part they were just petty notes. In fact, they rarely had anything at all to do with the war. Then again, dwelling on the war even in his free time was bad for a soldier. Hughes and Roy had joked back and forth, poking fun at each other. Occasionally Hughes would code important information into the letters in the form of bad jokes, and it had saved Roy a lot of trouble, even his life, on several occasions. He had also been the first to notice how the red stones given to the alchemists seemed to be driving many of them mad. Roy had been stationed near Zolof Kimbley when he finally snapped, killing civilians and soldiers indiscriminately. If it hadn't been for Hughes' warning, he might have been among those he had turned into living bombs. He had also worn the ring as little as possible at Hughes' urging. In addition to the effects it had on the mind, the rebound from using it too often had already taken its toll on several of the alchemists. Roy often wondered how he would have ever survived the war without Hughes' protection. Never underestimate the importance of a good intelligence officer.

Subconsciously or not, after a few hours Roy found himself wading through a box of his old research papers, especially those from his darker days after the war in Ishbar. After Marcoh's visit, he had thrown himself into the research in search of a way to restore those lives he had taken in the war. Since the victorious side does not try its own soldiers for war crimes, the force of Mustang's conscience had taken over the job. The atrocities he had committed under the premise of just "following orders" haunted him, pushing him into darker and darker corners of his research. If it had not been for Maes Hughes, Roy realized, he probably would have worked himself to death, or worse. He had come to visit, and somehow talked him out of his self-blaming reverie. During those days, his apartment was probably the creepiest it had ever been. Earlier that week, he had gotten buckets of blood from the butcher, intent on testing the effectiveness of blood arrays versus other methods. He never got far in his research though, always fearing the consequences, Marcoh's dire warnings echoing in the back of his head. But it was still no reason not to push the research itself forward. If he caught up with the research the government had been doing covertly, maybe he could do something about it. Hughes, however, saw through his excuses. Sometimes his perception was uncanny, for the man did not look like he should be so clever. Undoubtedly a trick the intelligence people picked up.

"_Look, you know I don't understand alchemy. But this is dangerous. I know you're researching that taboo, I can see it behind your eyes... Don't Roy. Just don't. The world doesn't need another crazed scientist. We need someone to lead us out of this mess."_

Hughes' trust had been his inspiration to rise up through the military ranks, to actually _do_ something about the problems he saw, rather than wallow in his own misery. He had decided then, rather than try to out-research the military on his own he would put a stop to the research itself. Make sure no one tried such desperate things. The leap of logic was shaky at first, but with Hughes' support behind him, his resolve soon solidified.

--

Mustang stood, stretched, and looked around. He forced a smile to prove to himself that he could still do it, and realized that in the end, the last thing Hughes would want would be for him to sacrifice everything just to bring him back. Maes Hughes had always been the self-sacrificing type, putting everyone before himself. Had Hughes not used his connections to help making a firm base for Roy to stand on, he would be nowhere near where he was today. It wasn't worth sacrificing all of that work, was it? But then there was his family. Work left unfinished. His most important, most treasured work.

The shrill ring of the telephone startled Mustang out of his stream of circular reasoning. Stepping out in the hallway of his apartment, he blinked to adjust his eyes to the normal lighting. Squinting into the fluorescent glow of his lights, he answered the phone.

"Yes?"

"Colonel, sir." Over the phone, Mustang could hear him straighten up to attention. "There's a problem at the lab we think you should know about." Mustang nodded, snapping back into his military mindset as the caller continued quickly, clearly very nervous. "We know that you've intentionally distanced yourself from the investigation at the fifth laboratory, but there has been some very suspicious activity around there lately. You were... actually the only one we knew we could call this late," the soldier added rather sheepishly.

"Go on," Mustang commanded, sighing inwardly. Hearing about the fifth lab now made his mood much worse, but he couldn't bee seen as shirking his duty, even at two in the morning.

"We're almost certain that there is someone else in the labs, sir. A few of the men have seen him, or it, or whatever it is, wandering the place at night when there are fewer guards around. Now, I know we weren't supposed to, but a few of the intelligence guys were looking through the records, and this thing isn't a chimera or anything else they were making here. Unless it's a ghost, ha ha. Errr... anyway, sir if you could come yourself and just take a look at this, maybe you'd have some more insight on it than we do."

Mustang nodded again, not really realizing no one was around to see. He assured the man he'd be there shortly, and ended the call. Two seconds later, he picked up the receiver and dialled his first lieutenant, telling her to meet him at the fifth lab as soon as she could.

--

Outside the lab, two soldiers were standing on guard, flanking the entrance. Roy nodded to them and continued through. More often than not, just flashing the array on the back of his gloves at the guards was enough to gain entrance to facilities. His reputation often preceded him, and most of the regular soldiers were wary of his smug demeanour and fiery temper. Normally he'd stop to warn the guards to be more careful about letting people without credentials inside, but he was in a hurry to disprove whatever had spooked the men and then head back to his apartment. He was more than a little apprehensive about what the intelligence men could have put their noses into. Making a connection between this lab and the chimera lab Marcoh had spoken of, Mustang feared the worst.

Inside, the lab was the same mess of rubble and ruined experiments it had been when he visited it last. Inside he knew that FullMetal and his brother had fought two men whose souls had also been affixed to armour. Absentmindedly, Roy wondered what price the alchemists who had performed the transmutation had had to pay. Or had they used the red stone instead? The law of equivalent trade could be such a fluid thing, so impossible to nail down to one consistent equation of cost. Surely those convicts had not volunteered to have their souls torn from their bodies and attached to suits of armour? Then again, the lure of immortality could be strong, especially when the government is prepared to take your life away otherwise. Affixing a soul still carried a heavy price, though. Surely there was not enough of the red stone to pay for all of these experiments.

Turning his mind back to the task at hand, he stared intently at some of the ruins. FullMetal's manipulation of the stone on the floor was actually much more thorough than the sort of work Armstrong did. The spikes had been created so the hardest materials were not only on the outside, but woven through the inside as well to make it less hollow. Most alchemists didn't have the power to propel the weight. No wonder the boy was considered a genius. Entire pieces of the walls had been sacrificed to the reactions, and the explosion later on had done nothing to help. The entire building looked like it was ready to cave in on itself and, Roy thought to himself, he wouldn't be surprised if that had been part of the plan in the first place. As soon as the operation was discovered, the whole thing would fall in on itself, destroying the evidence. It was a very military thing to do.

Following one of the few clear hallways Colonel Mustang pushed himself fully into his military mindset, personal troubles forced into the deeper corners of his mind and, for the most part, ignored. They itched at the back of his mind though. He straightened his uniform and made his way into the main room. Thanks to its convenient location in the centre of the facility and relatively intact condition, it had been made into a sort of make-shift headquarters for the investigation of the labs. A few of the soldiers were standing around, looking only vaguely nervous while sipping coffee and picking over a box of stale doughnuts no doubt left over from the earlier shift. A few were telling tasteless jokes. When they noticed the colonel's entrance, they turned to salute.

"At ease," Mustang said with a weary nod, and most of the men returned to their quiet chatter. One in particular turned to approach Mustang, and with a quick salute tried to explain the situation.

"Colonel Mustang, sir," he saluted. "I'm Sgt. Davis. It seems I've drawn the short straw, so I suppose I need to explain the situation to you. We've all been in here for days searching for evidence of what was going on in here, and it wouldn't surprise me at all if we'd all gone nuts over it, but there are some things in here that we really think you need to see. There's just no explanation for them, and we all know that you're great at debunking the crazy theories everyone comes up with... So, if you could just follow me, hopefully you can come up with a logical explanation?" The man babbled with complete disregard to etiquette, forgetting to let the colonel make the suggestion to look things over. Roy just shrugged, however, and followed him to one of the remote labs on the outskirts of the facility.

The room was surprisingly well-lit, but the light seemed to be coming from the walls themselves, and the obscure alchemy arrays drawn on them. The soldier turned to face Mustang as he walked into the room, and watched as he wandered through, frowning at the various artefacts strewn about. Sgt. Davis soon grew bored of watching the Colonel filing through the papers in the room, and began to fidget.

"Sergeant," Mustang said, noticing the soldier's discomfort, "Go get me some coffee. This is going to take a while."

Most of the research papers left in the lab were coded. Looking over them, Mustang was amazed at the detail put into it. At first glance, most looked like any layperson's idea of actual alchemy research documents. They appeared to be about manipulating the elements like fire and water, though the arrays on the walls clearly showed that something entirely different was going on. Hiding things in plain sight again... Roy wondered exactly how deep Marcoh had been involved in the research. The was without a doubt his lab. Running his hand across one of the arrays, he shivered, a vague memory of its purpose surfacing in his mind. Body alchemy...

--

It was several more hours before Roy could leave the lab. Though he had told the soldiers that there was nothing to worry about, that the building was just falling apart, the experience had left him more wary than before. Too much had gone on in the lab that he didn't understand, that he was never meant to know about. Naturally he couldn't show his reactions with the men around, but outside in the cold early-morning hours he was shivering more than necessary. At this hour, the thought of sleep was pretty much useless; he would have to be back at the office in three hours.

With a sigh he sat down against the side of the building and stared off into the pale sunrise. Not for the first time that week, he considered taking up smoking. It wasn't like he'd ever need a lighter. In fact, he was sure he would have picked it up sooner if the lingering smell Havoc left in a room didn't irk him so. He took off his gloves and rubbed his hands together to keep them warm. He found it ironic that if he ever tried to warm his hands with his gloves on, he'd probably end up a good deal warmer than he'd intended. When he caught his eyelids forcing their way down, he stood up to stretch and decided what he really needed was breakfast, a cup of coffee, and something to take his mind off of things. As he walked back towards his car, the sound of gravel crunching under car tires startled him.

"Good morning, Colonel," Riza said with the best salute she could manage while driving. "I only got your message when I got up this morning. I had a feeling you'd still be here." Behind her eyes there was more concern that a first lieutenant usually has for a colonel, but she did her best to hide it.

"Morning Lt. Hawkeye," Roy replied, dropping the formalities. "Want to come to breakfast with me? I'll buy if you drive."

The offer was so blatant that Riza could do nothing but accept. However, there were few places in town where two people in uniform could sit and eat in peace. They ended up at a small corner diner, staring out of the booth towards the street. Central was a city that slept late, and the lack of activity on the streets forced Riza's attention onto Roy. She had ordered only a cup of coffee, so she watched him eat instead. He seemed paler than usual, and a bit scruffy. He clearly hadn't slept much, nor bothered to shave for a few days. He was beginning to take on the look of a vagrant or a wino, though the cleanly-pressed military uniform did enough to distract most other people from Roy's sorry state. He snapped out of his introspective daze only long enough to order a second omelette. Waiting for it to come, he nursed his coffee and stared at Riza. After a rather awkward minute, he broke the silence.

"What's it all about, really. When you get down to it?" The only sound was that of his coffee cup returning to the table.

"I'm sorry?"

"I've been thinking a lot this past week." He paused again, tracing his fingers along the grooves etched into the table. Unconsciously, his fingers began tracing mundane alchemical arrays. He caught himself, surprised. It had been years since he had done anything other than flame alchemy.

"Sir?"

The omelette arrived. Roy stared at it, poked it intently with his fork.

"What time is it?"

"7:30"

"We should go visit Gracia."

With that, he turned his attention entirely to his omelette. Without a word, he paid the check, and walked back out to the car. Riza followed close behind and, unable to come up with anything appropriate to say, drove on to the Hughes home in silence.

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(Author's Notes: Yeah... New Chapter 3 will hopefully be up soon, when I finally get this one evil sticky plot point worked out.

Fox of burden: Thank you so much for that long review! I'm still thinking about what to do for that part.. but don't worry, the thought of genitals never crossed my mind. (-: I'm not sure if my random plot point will work around it a bit, or just make things worse. It depends on how much I want to torutre Roy.

Sketchyheart: STOP STALKING ME. I was hiding this for a reason darnit. It's your fault I decided to go back and actually write this properly. Hehehe... actually... yeah, I'm just gonna blame you.

Darkest Aphelion: My first reviewer... merci! But what do you mean by "that Roy"?) 


	3. THIS CHAPTER DOES NOT EXIST RIGHT NOW

(Errr... I'm still writing/re-writing this chapter. Bear with me, sorry!)


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